I: pbuilder: network access will be disabled during build I: Current time: Sat May 6 03:48:41 +14 2023 I: pbuilder-time-stamp: 1683294521 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [readseq_1-14.dsc] I: copying [./readseq_1.orig.tar.gz] I: copying [./readseq_1-14.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Oct 31 09:23:42 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./readseq_1-14.dsc: no acceptable signature found dpkg-source: info: extracting readseq in readseq-1 dpkg-source: info: unpacking readseq_1.orig.tar.gz dpkg-source: info: unpacking readseq_1-14.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 20-Formats.patch dpkg-source: info: applying 20-Makefile.patch dpkg-source: info: applying 30-arb-code-patches.patch dpkg-source: info: applying 552830.patch dpkg-source: info: applying gcc-4.6_format-security.patch dpkg-source: info: applying enable_tests.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying buffer_overflow.patch dpkg-source: info: applying fix_tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/20725/tmp/hooks/D01_modify_environment starting debug: Running on ff4a. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 6 03:49 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/20725/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/20725/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=2e89d5bcd4434a14bba08660d51c5211 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=20725 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Lxsib6qj/pbuilderrc_0D3G --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Lxsib6qj/b2 --logfile b2/build.log --extrapackages usrmerge readseq_1-14.dsc' SUDO_GID=113 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 5.10.0-22-armmp-lpae #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash -rwxr-xr-x 1 root root 133220 Sep 21 2022 date -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd -rwxr-xr-x 1 root root 68104 Sep 21 2022 df -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 67548 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 May 6 03:49 sh -> /bin/bash -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch -rwxr-xr-x 1 root root 67548 Sep 21 2022 true -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/20725/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), ncbi-tools-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19329 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on ncbi-tools-dev; however: Package ncbi-tools-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libncbi6{a} libncbi6-dev{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} ncbi-data{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx ncbi-tools-bin wget 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 29.9 MB of archives. After unpacking 120 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf libncbi6 armhf 6.1.20170106+dfsg1-10 [3305 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libncbi6-dev armhf 6.1.20170106+dfsg1-10 [4943 kB] Fetched 29.9 MB in 2s (13.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19329 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../02-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../22-libelf1_0.188-2.1_armhf.deb ... Unpacking libelf1:armhf (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_armhf.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../30-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... Selecting previously unselected package libncbi6:armhf. Preparing to unpack .../31-libncbi6_6.1.20170106+dfsg1-10_armhf.deb ... Unpacking libncbi6:armhf (6.1.20170106+dfsg1-10) ... Selecting previously unselected package libncbi6-dev:armhf. Preparing to unpack .../32-libncbi6-dev_6.1.20170106+dfsg1-10_armhf.deb ... Unpacking libncbi6-dev:armhf (6.1.20170106+dfsg1-10) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-10) ... Setting up libicu72:armhf (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libncbi6:armhf (6.1.20170106+dfsg1-10) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libncbi6-dev:armhf (6.1.20170106+dfsg1-10) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/20725/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/20725/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/readseq-1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../readseq_1-14_source.changes dpkg-buildpackage: info: source package readseq dpkg-buildpackage: info: source version 1-14 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/build/readseq-1' rm -f *.o core test.* readseq make[1]: Leaving directory '/build/readseq-1' debian/rules override_dh_clean make[1]: Entering directory '/build/readseq-1' dh_clean rm -f readseq make[1]: Leaving directory '/build/readseq-1' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/readseq-1' Compiling readseq with NCBI toolkit support and ARB patches gcc -o readseq -I/usr/include/ncbi -g -O2 -ffile-prefix-map=/build/readseq-1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -DNCBI -I/usr/include/ncbi -DARB readseq.c ureadseq.c ureadasn.c -lncbi -lncbiobj -lncbicdr -lncbiacc -lncbitool -lncbimmdb -lncbiid1 -lnetcli -lm -Wl,-z,relro -Wl,-z,now readseq.c: In function 'formatstr': readseq.c:267:41: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 267 | case kASNseqset : return formats[kASN1-1]; | ~~~~~~~^~~~~~~~~ readseq.c:269:45: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 269 | case kPhylipSequential: return formats[kPhylip-1]; | ~~~~~~~^~~~~~~~~~~ readseq.c:273:22: warning: return discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 273 | else return formats[format-1]; | ~~~~~~~^~~~~~~~~~ readseq.c: In function 'Nlm_Main': readseq.c:801:5: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] 801 | gets(oname= onamestore); | ^~~~ | fgets readseq.c:936:33: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 936 | sprintf( stemp,"%s_%d", oname, whichSeq); | ~^ ~~~~~~~~ | | | | int long int | %ld readseq.c:938:48: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 938 | fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp); | ~^ ~~~~~~~~ | | | | int long int | %ld readseq.c:980:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | int | %ld 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~~~ | | | long int readseq.c:980:51: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | int | %ld 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~ | | | long int readseq.c:980:65: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 980 | fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, id= %s\n", | ~^ | | | unsigned int | %lX 981 | whichSeq, seqlen, checksum, formatstr(format), seqidptr); | ~~~~~~~~ | | | long unsigned int readseq.c:998:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); | ~^ ~ | | | | int long int | %ld readseq.c:998:56: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 998 | if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:999:39: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 999 | else fprintf(foo," %d %d YF\n", i, seqlen); | ~^ ~ | | | | int long int | %ld readseq.c:999:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 999 | else fprintf(foo," %d %d YF\n", i, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1117:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ | ~^ | | | int | %ld 1118 | cp, seqlen, timestr, checkall); | ~~~~~~ | | | long int readseq.c:1117:55: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long unsigned int' [-Wformat=] 1117 | fprintf(foo,"\n %s MSF: %d Type: N %s Check: %d ..\n\n", /* GSt + RL */ | ~^ | | | int | %ld 1118 | cp, seqlen, timestr, checkall); | ~~~~~~~~ | | | long unsigned int readseq.c:1133:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1133 | if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1134:28: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1134 | else fprintf(foo," %d %d YF\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld readseq.c:1158:49: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1158 | fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c: In function 'seqFileFormatFp': ureadseq.c:1535:19: warning: format '%d' expects argument of type 'int *', but argument 3 has type 'long int *' [-Wformat=] 1535 | sscanf( sp, "%d%d", &nspp, &nlen); | ~^ ~~~~~ | | | | int * long int * | %ld ureadseq.c:1535:21: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long int *' [-Wformat=] 1535 | sscanf( sp, "%d%d", &nspp, &nlen); | ~^ ~~~~~ | | | | int * long int * | %ld ureadseq.c: In function 'writeSeq': ureadseq.c:1784:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1784 | sprintf(numform, "%d", seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1813:43: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1813 | fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1814:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1814:48: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1814 | fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1828:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1828:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1828 | fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1838:53: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1838 | for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j); | ~~~^ ~ | | | | | long int | int | %10ld ureadseq.c:1848:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1848:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1848 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1857:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1857:41: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1857 | fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1858:37: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1858 | fprintf(outf,"SQ %d BP\n", seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1869:38: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1869:58: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 1869 | fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); | ~^ ~~~~~~~~ | | | | int long unsigned int | %ld ureadseq.c:1878:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1878:52: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1878 | fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1884:26: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1884:36: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1884 | fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1915:53: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1915 | fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, seqlen); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1937:41: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); | ~~^ ~~~~~~ | | | | int long int | %6ld ureadseq.c:1937:53: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1937 | fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); | ~~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %8lX ureadseq.c:1954:42: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); | ~~^ ~~~~~~ | | | | int long int | %6ld ureadseq.c:1954:54: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1954 | fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); | ~~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %8lX ureadseq.c:1960:40: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", | ~~^ | | | int | %6ld 1961 | idword, seqlen, checksum); | ~~~~~~ | | | long int ureadseq.c:1960:52: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=] 1960 | fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", | ~~^ | | | int | %5ld 1961 | idword, seqlen, checksum); | ~~~~~~~~ | | | long unsigned int ureadseq.c:1972:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:1972:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 1972 | fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:1979:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 1979 | fprintf(outf,"%4d %-60s\n",seqlen,seqname); | ~~^ ~~~~~~ | | | | int long int | %4ld ureadseq.c:2002:27: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~ | | | | int long int | %ld ureadseq.c:2002:37: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=] 2002 | fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); | ~^ ~~~~~~~~ | | | | unsigned int long unsigned int | %lX ureadseq.c:2043:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 2043 | if (numline==1) fprintf(outf,"%-9d ",i+1); | ~~~^ ~~~ | | | | int long int | %-9ld ureadseq.c: In function 'readPAUPinterleaved': ureadseq.c:213:22: warning: '%s' directive writing up to 255 bytes into a region of size between 246 and 251 [-Wformat-overflow=] 213 | sprintf(si, " %d) %s\n", V->nseq, s); | ^~ In function 'addinfo', inlined from 'readPAUPinterleaved' at ureadseq.c:813:13: ureadseq.c:213:3: note: 'sprintf' output between 7 and 267 bytes into a destination of size 256 213 | sprintf(si, " %d) %s\n", V->nseq, s); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadseq.c: In function 'writeSeq': ureadseq.c:2007:45: warning: '%d' directive writing between 1 and 6 bytes into a region of size between 2 and 7 [-Wformat-overflow=] 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~ ureadseq.c:2007:39: note: directive argument in the range [-32768, 32767] 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~~~~~~~~~~ ureadseq.c:2007:21: note: 'sprintf' output between 7 and 17 bytes into a destination of size 10 2007 | if (*nameform==0) sprintf(nameform, "%%%d.%ds ",namewidth,namewidth); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c: In function 'listASNSeqs': ureadasn.c:189:24: warning: passing argument 1 of 'AsnIoOpen' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 189 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit; | ^~~~~~~~ In file included from /usr/include/ncbi/ncbi.h:57, from ureadasn.c:13: /usr/include/ncbi/asn.h:384:54: note: expected 'Nlm_CharPtr' {aka 'char *'} but argument is of type 'const char *' 384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode)); /usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro 'PROTO' 192 | #define PROTO(x) x /* Prototypes are acceptable */ | ^ ureadasn.c: In function 'readASNSeq': ureadasn.c:261:24: warning: passing argument 1 of 'AsnIoOpen' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 261 | if ((aip = AsnIoOpen(filename, inIsBinary?"rb":"r")) == NULL) goto errxit; | ^~~~~~~~ /usr/include/ncbi/asn.h:384:54: note: expected 'Nlm_CharPtr' {aka 'char *'} but argument is of type 'const char *' 384 | NLM_EXTERN AsnIoPtr LIBCALL AsnIoOpen PROTO((CharPtr file_name, CharPtr mode)); /usr/include/ncbi/ncbilcl.h:192:18: note: in definition of macro 'PROTO' 192 | #define PROTO(x) x /* Prototypes are acceptable */ | ^ ureadasn.c:262:31: warning: 'fgets' writing 255 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=] 262 | for (i=0; ifp); /* this may mess up asn routines... */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c:241:15: note: destination object 'stemp' of size 200 241 | char *seq, stemp[200]; | ^~~~~ In file included from ureadasn.c:8: /usr/include/stdio.h:592:14: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 592 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ ureadasn.c:262:31: warning: 'fgets' writing 255 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=] 262 | for (i=0; ifp); /* this may mess up asn routines... */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c:241:15: note: destination object 'stemp' of size 200 241 | char *seq, stemp[200]; | ^~~~~ /usr/include/stdio.h:592:14: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 592 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ ureadasn.c:262:31: warning: 'fgets' writing 255 bytes into a region of size 200 overflows the destination [-Wstringop-overflow=] 262 | for (i=0; ifp); /* this may mess up asn routines... */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ureadasn.c:241:15: note: destination object 'stemp' of size 200 241 | char *seq, stemp[200]; | ^~~~~ /usr/include/stdio.h:592:14: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 592 | extern char *fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ /usr/bin/ld: /tmp/ccaW9t25.o: in function `Nlm_Main': ./readseq.c:783: warning: the use of `tmpnam' is dangerous, better use `mkstemp' /usr/bin/ld: ./readseq.c:801: warning: the `gets' function is dangerous and should not be used. make[1]: Leaving directory '/build/readseq-1' dh_auto_test make -j4 test make[1]: Entering directory '/build/readseq-1' Test for general read/write of all chars: ./readseq -p alphabet.std -otest.alpha diff test.alpha alphabet.std Test for valid format conversions: ./readseq -v -p -f=ig nucleic.std -otest.ig Sequence 1, length= 228, checksum= 1B5655D0, format= 20. Vienna, id= nucleic/amino test ./readseq -v -p -f=gb test.ig -otest.gb Sequence 1, length= 228, checksum= 1B5655D0, format= 1. IG/Stanford, id= nucleic/amino ./readseq -v -p -f=nbrf test.gb -otest.nbrf Sequence 1, length= 228, checksum= 1B5655D0, format= 2. GenBank/GB, id= nucleic/amino 228 bp ./readseq -v -p -f=embl test.nbrf -otest.embl Sequence 1, length= 228, checksum= 1B5655D0, format= 3. NBRF, id= nucleic/amino ./readseq -v -p -f=gcg test.embl -otest.gcg Sequence 1, length= 228, checksum= 1B5655D0, format= 4. EMBL, id= nucleic/amino ./readseq -v -p -f=strider test.gcg -otest.strider Sequence 1, length= 228, checksum= 1B5655D0, format= 5. GCG, id= nucleic/amino ./readseq -v -p -f=fitch test.strider -otest.fitch Sequence 1, length= 228, checksum= 1B5655D0, format= 6. DNAStrider, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=fasta test.fitch -otest.fasta Sequence 1, length= 228, checksum= 1B5655D0, format= 7. Fitch, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=pir test.fasta -otest.pir Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=ig test.pir -otest.ig-b Sequence 1, length= 228, checksum= 1B5655D0, format= 14. PIR/CODATA, id= nucleic/amino, diff test.ig test.ig-b 1,2c1,2 < ;nucleic/amino test, 228 bases, 1B5655D0 checksum. < nucleic/amino --- > ;nucleic/amino, , 228 bases, 1B5655D0 checksum. > nucleic/amino, make[1]: [Makefile:70: test] Error 1 (ignored) Test for multiple-sequence format conversions: ./readseq -p -f=ig multi.std -otest.m-ig ./readseq -p -f=gb test.m-ig -otest.m-gb ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf ./readseq -p -f=embl test.m-nbrf -otest.m-embl ./readseq -p -f=fasta test.m-embl -otest.m-fasta ./readseq -p -f=pir test.m-fasta -otest.m-pir ./readseq -p -f=msf test.m-pir -otest.m-msf ./readseq -p -f=paup test.m-msf -otest.m-paup ./readseq -p -f=ig test.m-paup -otest.m-ig-b diff test.m-ig test.m-ig-b 1,2c1,2 < ;acarr58sst , 183 bases, 64754A4D checksum. < acarr58sst --- > ;acarr58ss, 183 bases, 64754A4D checksum. > acarr58ss 7c7 < ;amgrrbst , 183 bases, C886D2FB checksum. --- > ;amgrrbst, 183 bases, C886D2FB checksum. 13c13 < ;bmorrbst , 183 bases, 3E9C23D6 checksum. --- > ;bmorrbst, 183 bases, 3E9C23D6 checksum. 19c19 < ;crerrbst , 183 bases, AC88A337 checksum. --- > ;crerrbst, 183 bases, AC88A337 checksum. 25,26c25,26 < ;ddirr58sst , 183 bases, 1E3D23B8 checksum. < ddirr58sst --- > ;ddirr58ss, 183 bases, 1E3D23B8 checksum. > ddirr58ss make[1]: [Makefile:82: test] Error 1 (ignored) Expect differences in the header lines due to different format headers. If any sequence lines differ, or if the checksums differ, there is a problem. ---------------------- To clean up test files, command me: make clean make[1]: Leaving directory '/build/readseq-1' create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install --destdir=debian/readseq/ make -j4 install DESTDIR=/build/readseq-1/debian/readseq AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/readseq-1' install readseq /build/readseq-1/debian/readseq/usr/bin install *.std /build/readseq-1/debian/readseq/usr/share/doc/readseq/tests install Makefile /build/readseq-1/debian/readseq/usr/share/doc/readseq/tests make[1]: Leaving directory '/build/readseq-1' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'readseq' in '../readseq_1-14_armhf.deb'. dpkg-deb: building package 'readseq-dbgsym' in '../readseq-dbgsym_1-14_armhf.deb'. dpkg-genbuildinfo --build=binary -O../readseq_1-14_armhf.buildinfo dpkg-genchanges --build=binary -O../readseq_1-14_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/20725/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/20725/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/20725 and its subdirectories I: Current time: Sat May 6 03:50:24 +14 2023 I: pbuilder-time-stamp: 1683294624